<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000066">
<div class="moz-cite-prefix">Hello,<br>
<br>
I got lost in this topic.<br>
So if I understand well.. to fix the VEP forking issue I must can
re-download the VEP script from ensembl website?<br>
<br>
Thank you !<br>
<br>
Best regards,<br>
Guillermo.<br>
<br>
On 05/15/2013 01:35 PM, Will McLaren wrote:<br>
</div>
<blockquote
cite="mid:CAMVEDX2FYMGmikPzvvAwyhGh6okpEnkC=3axo2aeaLmuKCi+NA@mail.gmail.com"
type="cite">
<div dir="ltr">This is now fixed on branch and head too.
<div><br>
</div>
<div style="">Will</div>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On 14 May 2013 17:30, Duarte Molha <span
dir="ltr"><<a moz-do-not-send="true"
href="mailto:duartemolha@gmail.com" target="_blank">duartemolha@gmail.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">Sorry Will... today you have loads of people
bugging you :-)
<div><br>
</div>
<div>I just updated to the latest VEP you pointed me to
... and now the fail in on line 1307</div>
<div><br>
</div>
<div>
<div>Use of uninitialized value $line in join or string
at
/NGS_Test/duarte/vep_71/Bio/EnsEMBL/Variation/Utils/VEP.pm
line 1307.</div>
<div><br>
</div>
<div>Cheers</div>
<span class="HOEnZb"><font color="#888888">
<div><br>
Duarte</div>
<div><br>
</div>
</font></span></div>
</div>
<div class="gmail_extra">
<div class="im"><br clear="all">
<div><font style="" color="#999999">=========================<br>
Duarte Miguel Paulo Molha <br>
</font>
<div><font style="" color="#999999"> <a
moz-do-not-send="true"
href="http://about.me/duarte" target="_blank">http://about.me/duarte</a>
<br>
=========================</font></div>
</div>
<br>
<br>
</div>
<div>
<div class="h5">
<div class="gmail_quote">On Tue, May 14, 2013 at 4:26
PM, Will McLaren <span dir="ltr"><<a
moz-do-not-send="true"
href="mailto:wm2@ebi.ac.uk" target="_blank">wm2@ebi.ac.uk</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">Hi Duarte,
<div><br>
</div>
<div>You are correct, it was the --individual
flag causing the problem.</div>
<div><br>
</div>
<div>I have committed a fix to the 71 branch
(does not include forking fixes) and to head
(does include forking fixes, download from <a
moz-do-not-send="true"
href="http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/ensembl-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm?revision=1.94&root=ensembl"
target="_blank">http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/ensembl-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm?revision=1.94&root=ensembl</a>).</div>
<div><br>
</div>
<div>Regards</div>
<span><font color="#888888">
<div><br>
</div>
<div>Will</div>
</font></span></div>
<div>
<div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">
On 14 May 2013 15:17, Duarte Molha <span
dir="ltr"><<a moz-do-not-send="true"
href="mailto:duartemolha@gmail.com"
target="_blank">duartemolha@gmail.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote"
style="margin:0 0 0 .8ex;border-left:1px
#ccc solid;padding-left:1ex">
<div dir="ltr">However I believe it must
be something related to the <span
style="background-color:rgb(240,240,240);color:rgb(51,51,51);font-family:'Courier
New',Courier,monospace;font-size:13px;line-height:16px">--individual
[all|ind list] flag</span>
<div>
And does not seem to be related to
the --forks argument since it also
thoughs that error when running
single threaded. </div>
<div><br>
</div>
<div>However in single thread mode it
simply displays the error and keeps
going and with multiple forks the
process dies entirely.</div>
<div>
<div>My vcf contains 3 samples
genotypes and I have included the
--individual all option. <br>
</div>
<div><br>
</div>
<div>Best regards</div>
</div>
<span><font color="#888888">
<div>Duarte</div>
<div><br>
</div>
</font></span></div>
<div class="gmail_extra">
<div><br clear="all">
<div><font color="#999999">=========================<br>
Duarte Miguel Paulo Molha
<br>
</font>
<div><font color="#999999">
<a moz-do-not-send="true"
href="http://about.me/duarte"
target="_blank">http://about.me/duarte</a>
<br>
=========================</font></div>
</div>
<br>
<br>
</div>
<div>
<div>
<div class="gmail_quote">On Tue,
May 14, 2013 at 2:00 PM, Duarte
Molha <span dir="ltr"><<a
moz-do-not-send="true"
href="mailto:duartemolha@gmail.com"
target="_blank">duartemolha@gmail.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote"
style="margin:0 0 0
.8ex;border-left:1px #ccc
solid;padding-left:1ex">
<div dir="ltr">Hi Will
<div><br>
</div>
<div>Unfortunately the
script does not report
in which line it fails and
I cannot provide you with
the entire file since it
is private data.</div>
<div>Is there a way of
reporting the line ></div>
<div><br>
</div>
<div>Thanks</div>
<span><font color="#888888">
<div><br>
Duarte</div>
<div><br>
</div>
</font></span></div>
<div class="gmail_extra">
<div><br clear="all">
<div><font color="#999999">=========================<br>
Duarte Miguel
Paulo Molha <br>
</font>
<div><font
color="#999999">
<a
moz-do-not-send="true"
href="http://about.me/duarte" target="_blank">http://about.me/duarte</a>
<br>
=========================</font></div>
</div>
<br>
<br>
</div>
<div>
<div>
<div class="gmail_quote">On
Tue, May 14, 2013 at
1:05 PM, Will McLaren
<span dir="ltr"><<a
moz-do-not-send="true" href="mailto:wm2@ebi.ac.uk" target="_blank">wm2@ebi.ac.uk</a>></span>
wrote:<br>
<blockquote
class="gmail_quote"
style="margin:0 0 0
.8ex;border-left:1px
#ccc
solid;padding-left:1ex">
<div dir="ltr">Hi
Duarte,
<div><br>
Do you have some
input that
causes this
error?</div>
<div><br>
</div>
<div>Thanks</div>
<span><font
color="#888888">
<div><br>
</div>
<div>Will</div>
</font></span></div>
<div>
<div>
<div
class="gmail_extra"><br>
<br>
<div
class="gmail_quote">
On 14 May 2013
12:57, Duarte
Molha <span
dir="ltr"><<a
moz-do-not-send="true" href="mailto:duartemolha@gmail.com"
target="_blank">duartemolha@gmail.com</a>></span>
wrote:<br>
<blockquote
class="gmail_quote"
style="margin:0
0 0
.8ex;border-left:1px
#ccc
solid;padding-left:1ex">
<div dir="ltr">Another
bug using the
updated
version... now
using the
--check_alleles
and
--check_existing
options the
script dies at
line 4759
<div><br>
</div>
<div>
<div>Use of
uninitialized
value in
string ne at
/NGS_Test/duarte/vep_71/Bio/EnsEMBL/Variation/Utils/VEP.pm
line 4759.</div>
</div>
<div><br>
</div>
<div><br>
</div>
<div>Best
regards</div>
<span><font
color="#888888">
<div><br>
</div>
<div>Duarte</div>
</font></span></div>
<div
class="gmail_extra">
<div><br
clear="all">
<div><font
color="#999999">=========================<br>
Duarte
Miguel Paulo
Molha <br>
</font>
<div><font
color="#999999">
<a
moz-do-not-send="true"
href="http://about.me/duarte" target="_blank">http://about.me/duarte</a>
<br>
=========================</font></div>
</div>
<br>
<br>
</div>
<div>
<div>
<div
class="gmail_quote">On
Tue, May 14,
2013 at 11:22
AM, Will
McLaren <span
dir="ltr"><<a
moz-do-not-send="true" href="mailto:wm2@ebi.ac.uk" target="_blank">wm2@ebi.ac.uk</a>></span>
wrote:<br>
<blockquote
class="gmail_quote"
style="margin:0
0 0
.8ex;border-left:1px
#ccc
solid;padding-left:1ex">
<div dir="ltr">Thanks
- try <a
moz-do-not-send="true"
href="http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/ensembl-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm?revision=1.93&root=ensembl"
target="_blank">http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/ensembl-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm?revision=1.93&root=ensembl</a><span><font
color="#888888">
<div>
<br>
</div>
<div>Will</div>
</font></span></div>
<div>
<div>
<div
class="gmail_extra"><br>
<br>
<div
class="gmail_quote">On
14 May 2013
11:09, Duarte
Molha <span
dir="ltr"><<a
moz-do-not-send="true" href="mailto:duartemolha@gmail.com"
target="_blank">duartemolha@gmail.com</a>></span>
wrote:<br>
<blockquote
class="gmail_quote"
style="margin:0
0 0
.8ex;border-left:1px
#ccc
solid;padding-left:1ex">
<div dir="ltr">It
seems the
problems are
still there :
<div><br>
</div>
<div>Here is
my output:</div>
<div><br>
</div>
<div>
<div>
perl <a
moz-do-not-send="true"
href="http://variant_effect_predictor.pl" target="_blank">variant_effect_predictor.pl</a>
--config
vep_human.ini
-i INPUT.vcf
--fork 16</div>
<div><br>
</div>
<div>2013-05-14
10:33:38 -
Read
configuration
from
vep_human.ini</div>
<div>#----------------------------------#</div>
<div># ENSEMBL
VARIANT EFFECT
PREDICTOR #</div>
<div>#----------------------------------#</div>
<div><br>
</div>
<div>version
71</div>
<div><br>
</div>
<div>By Will
McLaren (<a
moz-do-not-send="true"
href="mailto:wm2@ebi.ac.uk" target="_blank">wm2@ebi.ac.uk</a>)</div>
<div><br>
</div>
<div>Configuration
options:</div>
<div><br>
</div>
<div>###</div>
<div>allow_non_variant
1</div>
<div>buffer_size
500000</div>
<div>cache
1</div>
<div>canonical
1</div>
<div>ccds
1</div>
<div>check_alleles
1</div>
<div>check_existing
1</div>
<div>config
vep_human.ini</div>
<div>core_type
core</div>
<div>custom
/ReferenceData/vep_additional_annotations/Somatic_variation_phenotypes.bed.gz,Somatic,bed,exact
</div>
<div>
/ReferenceData/vep_additional_annotations/dbsnp135_ensembl_variation_phenotype.bed.gz,dbsnp135,bed,exact</div>
<div>dir
/ReferenceData/vep_cache/</div>
<div>domains
1</div>
<div>force_overwrite
1</div>
<div>fork
16</div>
<div>gmaf
1</div>
<div>hgnc
1</div>
<div>host
<a
moz-do-not-send="true" href="http://ensembldb.ensembl.org"
target="_blank">ensembldb.ensembl.org</a></div>
<div>individual
all</div>
<div>input_file
INPUT.vcf</div>
<div>numbers
1</div>
<div>plugin
Blosum62
Condel,/ReferenceData/vep_cache/Plugins/config/Condel/config,b
Carol</div>
<div>polyphen
b</div>
<div>port
5306</div>
<div>protein
1</div>
<div>regulatory
1</div>
<div>sift
b</div>
<div>species
homo_sapiens</div>
<div>stats
HASH(0x35a8000)</div>
<div>terms
SO</div>
<div>toplevel_dir
/ReferenceData/vep_cache/</div>
<div>verbose
1</div>
<div>xref_refseq
1</div>
<div><br>
</div>
<div>--------------------</div>
<div><br>
</div>
<div>
Will only load
v71 databases</div>
<div>Species
'homo_sapiens'
loaded from
database
'homo_sapiens_core_71_37'</div>
<div>Species
'homo_sapiens'
loaded from
database
'homo_sapiens_cdna_71_37'</div>
<div>Species
'homo_sapiens'
loaded from
database
'homo_sapiens_vega_71_37'</div>
<div>Species
'homo_sapiens'
loaded from
database
'homo_sapiens_otherfeatures_71_37'</div>
<div>Species
'homo_sapiens'
loaded from
database
'homo_sapiens_rnaseq_71_37'</div>
<div>homo_sapiens_variation_71_37
loaded</div>
<div>homo_sapiens_funcgen_71_37
loaded</div>
<div>Bio::EnsEMBL::Compara::DBSQL::DBAdaptor
not found so
the following
compara
databases will
be ignored:
ensembl_compara_71</div>
<div>ensembl_ancestral_71
loaded</div>
<div>ensembl_ontology_71
loaded</div>
<div>2013-05-14
10:33:39 -
Connected to
core version
71 database
and variation
version 71
database</div>
<div>2013-05-14
10:33:39 -
Read existing
cache info</div>
<div>2013-05-14
10:33:39 -
Loaded plugin:
Blosum62</div>
<div>2013-05-14
10:33:39 -
Loaded plugin:
Condel</div>
<div>2013-05-14
10:33:39 -
Loaded plugin:
Carol</div>
<div>2013-05-14
10:33:40 -
Starting...</div>
<div>2013-05-14
10:33:40 -
Detected
format of
input file as
vcf</div>
<div>2013-05-14
10:33:46 -
Read 195789
variants into
buffer</div>
<div>2013-05-14
10:33:46 -
Skipping 67552
non-variant
loci</div>
<div>2013-05-14
10:33:46 -
Reading
transcript
data from
cache and/or
database</div>
<div>[======================================================================================================]
[ 100% ]</div>
<div>2013-05-14
10:40:19 -
Retrieved
189344
transcripts (0
mem, 202901
cached, 0 DB,
13557
duplicates)</div>
<div>2013-05-14
10:40:19 -
Reading
regulatory
data from
cache and/or
database</div>
<div>[======================================================================================================]
[ 100% ]</div>
<div>2013-05-14
10:50:09 -
Retrieved
872092
regulatory
features (0
mem, 872351
cached, 0 DB,
259
duplicates)</div>
<div>2013-05-14
10:50:12 -
Calculating
consequences</div>
<div>Use of
uninitialized
value $_ in
pattern match
(m//) at
/NGS_Test/duarte/vep_71/Bio/EnsEMBL/Variation/Utils/VEP.pm
line 1022.</div>
<div>Use of
uninitialized
value $_ in
pattern match
(m//) at
/NGS_Test/duarte/vep_71/Bio/EnsEMBL/Variation/Utils/VEP.pm
line 1030.</div>
<div>Use of
uninitialized
value $_ in
pattern match
(m//) at
/NGS_Test/duarte/vep_71/Bio/EnsEMBL/Variation/Utils/VEP.pm
line 1037.</div>
<div>Use of
uninitialized
value $_ in
pattern match
(m//) at
/NGS_Test/duarte/vep_71/Bio/EnsEMBL/Variation/Utils/VEP.pm
line 1089.</div>
<div>Use of
uninitialized
value $_ in
concatenation
(.) or string
at
/NGS_Test/duarte/vep_71/Bio/EnsEMBL/Variation/Utils/VEP.pm
line 1097.</div>
<div><br>
</div>
<div>ERROR:
Forked process
failed</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
</div>
</div>
<div
class="gmail_extra">
<div><br
clear="all">
<div><font
color="#999999">=========================<br>
Duarte
Miguel Paulo
Molha <br>
</font>
<div><font
color="#999999">
<a
moz-do-not-send="true"
href="http://about.me/duarte" target="_blank">http://about.me/duarte</a>
<br>
=========================</font></div>
</div>
<br>
<br>
</div>
<div>
<div>
<div
class="gmail_quote">On
Tue, May 14,
2013 at 10:42
AM, Duarte
Molha <span
dir="ltr"><<a
moz-do-not-send="true" href="mailto:duartemolha@gmail.com"
target="_blank">duartemolha@gmail.com</a>></span>
wrote:<br>
<blockquote
class="gmail_quote"
style="margin:0
0 0
.8ex;border-left:1px
#ccc
solid;padding-left:1ex">
<div dir="ltr">Thanks
<div><br>
</div>
<div>Running a
annotation
using 16
forks... lets
see how it
handles :)</div>
<div>I'll
report back
any issues.</div>
<div><br>
</div>
<div>Thanks
for the update</div>
<span><font
color="#888888">
<div><br>
</div>
<div>Duarte</div>
<div><br>
</div>
</font></span></div>
<div
class="gmail_extra">
<div><br
clear="all">
<div><font
color="#999999">=========================<br>
Duarte
Miguel Paulo
Molha <br>
</font>
<div><font
color="#999999">
<a
moz-do-not-send="true"
href="http://about.me/duarte" target="_blank">http://about.me/duarte</a>
<br>
=========================</font></div>
</div>
<br>
<br>
</div>
<div>
<div>
<div
class="gmail_quote">On
Tue, May 14,
2013 at 10:16
AM, Will
McLaren <span
dir="ltr"><<a
moz-do-not-send="true" href="mailto:wm2@ebi.ac.uk" target="_blank">wm2@ebi.ac.uk</a>></span>
wrote:<br>
<blockquote
class="gmail_quote"
style="margin:0
0 0
.8ex;border-left:1px
#ccc
solid;padding-left:1ex">
<div dir="ltr">Stuart,
Guillermo,
Duarte,
<div><br>
</div>
<div>I'm
currently
working on
some code as I
stated above
to improve
stability and
performance
under forking.</div>
<div><br>
</div>
<div>I've
committed some
code to the
HEAD of our
CVS tree which
should help
the problems
you are
encountering.
You'd all be
welcome to
test this out,
with the
obvious
proviso that
this is
development
code and may
contain bugs!</div>
<div><br>
</div>
<div>To use
this, you
should
download the
copy of VEP.pm
from:</div>
<div><br>
</div>
<div><a
moz-do-not-send="true"
href="http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/ensembl-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm?revision=1.92&root=ensembl"
target="_blank">http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/ensembl-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm?revision=1.92&root=ensembl</a><br>
</div>
<div><br>
</div>
<div>and
replace the
VEP.pm under
ensembl-variation/modules/Bio/EnsEMBL/Variation/Utils
(or just
Bio/EnsEMBL/Variation/Utils
if you use
INSTALL.pl)
with this one.</div>
<div><br>
</div>
<div>This code
will appear in
production in
the next
proper release
of Ensembl.</div>
<div><br>
</div>
<div>Regards</div>
<span><font
color="#888888">
<div><br>
</div>
<div>Will</div>
</font></span></div>
<div>
<div>
<div
class="gmail_extra"><br>
<br>
<div
class="gmail_quote">
On 14 May 2013
09:55, Stuart
Meacham <span
dir="ltr"><<a
moz-do-not-send="true" href="mailto:sm766@cam.ac.uk" target="_blank">sm766@cam.ac.uk</a>></span>
wrote:<br>
<blockquote
class="gmail_quote"
style="margin:0
0 0
.8ex;border-left:1px
#ccc
solid;padding-left:1ex">
<div
bgcolor="#FFFFFF"
text="#000000">
<div>Hi,<br>
<br>
I certainly
don't want to
hijack this
thread but it
seemed daft to
start another.
I am also
getting
forking
errors. I
don't use any
custom plugins
and am using a
validated VCF
as input (with
about 600,000
variants).
Trying to fork
more than 4
threads is
unstable even
on my machine
which has 64
cores and half
a TB of RAM.<br>
<br>
I haven't
found anything
reproducible,
however if I
do I'll report
back to the
list.<br>
<br>
Thanks<span><font
color="#888888"><br>
<br>
Stuart</font></span>
<div>
<div><br>
<br>
On 14/05/2013
09:42, Will
McLaren wrote:<br>
</div>
</div>
</div>
<div>
<div>
<blockquote
type="cite">
<div dir="ltr">Hello,
<div><br>
</div>
<div>Your
aa_grantham_distance
plugin is
somewhat
inefficient -
it retrieves
the peptide
alleles from
the HGVS
annotation,
which itself
requires some
database
fetching and
processing to
produce. This
is why it is
slow.</div>
<div><br>
</div>
<div>You can
get the
peptides from
the transcript
variation
object:</div>
<div><br>
</div>
<div>my @peps
= split "/",
$tva->transcript_variation->pep_allele_string();</div>
<div> <br>
</div>
<div>This will
give you
single-letter
AA codes, but
you could
either modify
your hash or
use BioPerl to
convert:</div>
<div><br>
</div>
<div><span
style="font-family:Arial,Helvetica,sans-serif;font-size:13px">$seqobj
=
Bio::PrimarySeq->new
( -seq =>
$single_letter_aa); </span><br
style="font-family:Arial,Helvetica,sans-serif;font-size:13px">
<span
style="font-family:Arial,Helvetica,sans-serif;font-size:13px">$three_letter_aa
=
Bio::SeqUtils->seq3($seqobj); </span><br>
</div>
<div><span
style="font-family:Arial,Helvetica,sans-serif;font-size:13px"><br>
</span></div>
<div><span
style="font-family:Arial,Helvetica,sans-serif;font-size:13px">You
should also
declare your
distances hash
in the new()
sub and store
it on $self;
this will also
marginally
speed up your
plugin.</span></div>
<div><span
style="font-family:Arial,Helvetica,sans-serif;font-size:13px"><br>
</span></div>
<div><span
style="font-family:Arial,Helvetica,sans-serif;font-size:13px">Regarding
the forking
issues, we are
working on
improving
stability
under forking.</span></div>
<div><span
style="font-family:Arial,Helvetica,sans-serif;font-size:13px"><br>
</span></div>
<div><span
style="font-family:Arial,Helvetica,sans-serif;font-size:13px">Thanks
for your
patience</span></div>
<div> <span
style="font-family:Arial,Helvetica,sans-serif;font-size:13px"><br>
</span></div>
<div><span
style="font-family:Arial,Helvetica,sans-serif;font-size:13px">Will</span></div>
</div>
<div
class="gmail_extra"><br>
<br>
<div
class="gmail_quote">
On 14 May 2013
07:37,
Guillermo
Marco Puche <span
dir="ltr"><<a
moz-do-not-send="true"
href="mailto:guillermo.marco@sistemasgenomicos.com"
target="_blank">guillermo.marco@sistemasgenomicos.com</a>></span>
wrote:<br>
<blockquote
class="gmail_quote"
style="margin:0
0 0
.8ex;border-left:1px
#ccc
solid;padding-left:1ex">
<div
bgcolor="#FFFFFF"
text="#000066">
<div>Hello,<br>
<br>
I'm not really
sure which one
of those
plugins is
causing the
fork error. I
cannot
recreate it
now running
each one of
them
separately.<br>
<br>
Here are both:<br>
<br>
<a
moz-do-not-send="true"
href="https://github.com/guillermomarco/vep_plugins_71" target="_blank">https://github.com/guillermomarco/vep_plugins_71</a><br>
<br>
They also slow
the
calculating
consequences
process a lot.
<a
moz-do-not-send="true"
href="http://aa_grantham_distance.pm" target="_blank">aa_grantham_distance.pm</a>
is just a
hardcoded
plugin from
one of the
biologists in
my work. It
was just a
pure copy
paste and
adaptation to
make it work
as a VEP
plugin. Maybe
the problem is
in the matrix
definition
every time the
sub routine is
called. I'm
not running
out of memory
nor CPU. I'm
currently
using it with
2 threads and
buffersize of
500 for a 5000
variant vcf
file.<br>
<br>
I'm my honest
opinion, I
think one (or
even both) of
those plugins
are slowing so
much the
calculating
process that
sometimes the
fork just
dies. Like
when you have
a timeout
during to
heavy network
traffic. So
when you use
them together
with lot of
other plugins
like Condel,
Consequence,
etc.. they may
be causing the
process to
handle and
die.<br>
<br>
Best regards,<br>
Guillermo.
<div>
<div><br>
<br>
On 05/13/2013
03:55 PM,
Duarte Molha
wrote:<br>
</div>
</div>
</div>
<div>
<div>
<blockquote
type="cite">
<div dir="ltr">I
also get this
error... it is
so prevalent
and
so difficult to
pinpoint what
is causing it
that I have
given up on
forking my
annotation
process.
<div><br>
</div>
<div>I do
think it is
related to the
number of
forks. It
seems to crash
less often if
you use a low
number of
forks...
anything above
5
will undoubtedly crash
the script at
least in my
experience.</div>
<div><br>
</div>
<div>Cheers</div>
<div><br>
Duarte</div>
</div>
<div
class="gmail_extra"><br
clear="all">
<div><font
color="#999999">=========================<br>
Duarte
Miguel Paulo
Molha <br>
</font>
<div><font
color="#999999">
<a
moz-do-not-send="true"
href="http://about.me/duarte" target="_blank">http://about.me/duarte</a>
<br>
=========================</font></div>
</div>
<br>
<br>
<div
class="gmail_quote">On
Mon, May 13,
2013 at 2:50
PM, Will
McLaren <span
dir="ltr"><<a
moz-do-not-send="true" href="mailto:wm2@ebi.ac.uk" target="_blank">wm2@ebi.ac.uk</a>></span>
wrote:<br>
<blockquote
class="gmail_quote"
style="margin:0
0 0
.8ex;border-left:1px
#ccc
solid;padding-left:1ex">
<div dir="ltr">Hi
Guillermo,
<div><br>
</div>
<div>Test each
plugin
individually
until you find
the one that
causes the
error. It is
highly
unlikely that
a particular
combination of
plugins is
causing the
crash.</div>
<div><br>
</div>
<div>Check
that there are
no "print" (to
STDOUT or
STDERR)
statements in
your plugin -
forking
assumes that
code remains
silent
otherwise it
will throw
errors like
this.</div>
<div><br>
</div>
<div> Also,
check what, if
anything, is
cached between
runs of your
plugin. If you
are caching
things (for
example to
avoid
re-querying a
database), you
may need to
write storable
hooks to
ensure the
data is
getting cached
between forks
- see <a
moz-do-not-send="true"
href="https://github.com/ensembl-variation/VEP_plugins/blob/master/ProteinSeqs.pm"
target="_blank">https://github.com/ensembl-variation/VEP_plugins/blob/master/ProteinSeqs.pm</a>
for an
example.</div>
<div><br>
</div>
<div>If you
still have no
luck, send me
the code and
an input file
that recreates
the problem.</div>
<div><br>
</div>
<div>Regards</div>
<div><br>
</div>
<div>Will</div>
</div>
<div
class="gmail_extra">
<br>
<br>
<div
class="gmail_quote">
<div>
<div>On 13 May
2013 13:18,
Guillermo
Marco Puche <span
dir="ltr"><<a
moz-do-not-send="true"
href="mailto:guillermo.marco@sistemasgenomicos.com"
target="_blank">guillermo.marco@sistemasgenomicos.com</a>></span>
wrote:<br>
</div>
</div>
<blockquote
class="gmail_quote"
style="margin:0
0 0
.8ex;border-left:1px
#ccc
solid;padding-left:1ex">
<div>
<div>
<div
bgcolor="#FFFFFF"
text="#000066">
Hello,<br>
<br>
I've started
to recently
having
problems with
VEP script
while using
different
plugins (most
of them own
plugins).<br>
<br>
<pre>2013-05-13 13:59:44 - Connected to core version 71 database and variation version 71 database
2013-05-13 13:59:44 - Loaded plugin: vcf_input
2013-05-13 13:59:44 - Loaded plugin: biobase
2013-05-13 13:59:44 - Loaded plugin: aa_grantham_distance
2013-05-13 13:59:44 - Loaded plugin: flanking_sequence
2013-05-13 13:59:44 - Loaded plugin: Condel
2013-05-13 13:59:44 - Output fields redefined (37 defined)
2013-05-13 13:59:44 - Starting...
2013-05-13 13:59:45 - Read 3888 variants into buffer
2013-05-13 13:59:54 - Reading transcript data from cache and/or database
[===============================================] [ 100% ]
2013-05-13 14:02:38 - Retrieved 6463 transcripts (0 mem, 0 cached, 13743 DB, 7280 duplicates)
2013-05-13 14:02:38 - Calculating consequences
[===================================> ] [ 78% ]
ERROR: Forked process failed
</pre>
I'm not
getting any
other error
message. So I
cannot debug
properly. I
thought my
plugins were
OK but it's
seems they
don't. I think
the problem
occurs when I
use
"aa_grantham_distance
plugin"
together with
"flanking_sequence".
I've no idea
what could be
causing this.<br>
<br>
I'm running
VEP on verbose
mode but I
can't get any
usefull
information.
How could I
debug that?<br>
<br>
Best regards,<br>
Guillermo.<br>
<br>
</div>
<br>
</div>
</div>
_______________________________________________<br>
Dev mailing
list <a
moz-do-not-send="true"
href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><br>
Posting
guidelines and
subscribe/unsubscribe
info: <a
moz-do-not-send="true"
href="http://lists.ensembl.org/mailman/listinfo/dev" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><br>
Ensembl Blog:
<a
moz-do-not-send="true"
href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a><br>
<br>
</blockquote>
</div>
</div>
</blockquote>
</div>
</div>
</blockquote>
</div>
</div>
</div>
<br>
_______________________________________________<br>
Dev mailing
list <a
moz-do-not-send="true"
href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><br>
Posting
guidelines and
subscribe/unsubscribe
info: <a
moz-do-not-send="true"
href="http://lists.ensembl.org/mailman/listinfo/dev" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><br>
Ensembl Blog:
<a
moz-do-not-send="true"
href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a><br>
<br>
</blockquote>
</div>
<br>
</div>
<br>
<fieldset></fieldset>
<br>
<pre>_______________________________________________
Dev mailing list <a moz-do-not-send="true" href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a>
Posting guidelines and subscribe/unsubscribe info: <a moz-do-not-send="true" href="http://lists.ensembl.org/mailman/listinfo/dev" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a>
Ensembl Blog: <a moz-do-not-send="true" href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a>
</pre>
</blockquote>
<br>
</div>
</div>
</div>
<br>
_______________________________________________<br>
Dev mailing
list <a
moz-do-not-send="true"
href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><br>
Posting
guidelines and
subscribe/unsubscribe
info: <a
moz-do-not-send="true"
href="http://lists.ensembl.org/mailman/listinfo/dev" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><br>
Ensembl Blog:
<a
moz-do-not-send="true"
href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a><br>
<br>
</blockquote>
</div>
<br>
</div>
</div>
</div>
<br>
_______________________________________________<br>
Dev mailing
list <a
moz-do-not-send="true"
href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><br>
Posting
guidelines and
subscribe/unsubscribe
info: <a
moz-do-not-send="true"
href="http://lists.ensembl.org/mailman/listinfo/dev" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><br>
Ensembl Blog:
<a
moz-do-not-send="true"
href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a><br>
<br>
</blockquote>
</div>
<br>
</div>
</div>
</div>
</blockquote>
</div>
<br>
</div>
</div>
</div>
<br>
_______________________________________________<br>
Dev mailing
list <a
moz-do-not-send="true"
href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><br>
Posting
guidelines and
subscribe/unsubscribe
info: <a
moz-do-not-send="true"
href="http://lists.ensembl.org/mailman/listinfo/dev" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><br>
Ensembl Blog:
<a
moz-do-not-send="true"
href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a><br>
<br>
</blockquote>
</div>
<br>
</div>
</div>
</div>
<br>
_______________________________________________<br>
Dev mailing
list <a
moz-do-not-send="true"
href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><br>
Posting
guidelines and
subscribe/unsubscribe
info: <a
moz-do-not-send="true"
href="http://lists.ensembl.org/mailman/listinfo/dev" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><br>
Ensembl Blog:
<a
moz-do-not-send="true"
href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a><br>
<br>
</blockquote>
</div>
<br>
</div>
</div>
</div>
<br>
_______________________________________________<br>
Dev mailing
list <a
moz-do-not-send="true"
href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><br>
Posting
guidelines and
subscribe/unsubscribe
info: <a
moz-do-not-send="true"
href="http://lists.ensembl.org/mailman/listinfo/dev" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><br>
Ensembl Blog:
<a
moz-do-not-send="true"
href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a><br>
<br>
</blockquote>
</div>
<br>
</div>
</div>
</div>
<br>
_______________________________________________<br>
Dev mailing list <a
moz-do-not-send="true" href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><br>
Posting guidelines
and
subscribe/unsubscribe
info: <a
moz-do-not-send="true"
href="http://lists.ensembl.org/mailman/listinfo/dev" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><br>
Ensembl Blog: <a
moz-do-not-send="true"
href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a><br>
<br>
</blockquote>
</div>
<br>
</div>
</div>
</div>
</blockquote>
</div>
<br>
</div>
</div>
</div>
<br>
_______________________________________________<br>
Dev mailing list <a
moz-do-not-send="true"
href="mailto:Dev@ensembl.org"
target="_blank">Dev@ensembl.org</a><br>
Posting guidelines and
subscribe/unsubscribe info: <a
moz-do-not-send="true"
href="http://lists.ensembl.org/mailman/listinfo/dev"
target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><br>
Ensembl Blog: <a moz-do-not-send="true"
href="http://www.ensembl.info/"
target="_blank">http://www.ensembl.info/</a><br>
<br>
</blockquote>
</div>
<br>
</div>
</div>
</div>
<br>
_______________________________________________<br>
Dev mailing list <a moz-do-not-send="true"
href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><br>
Posting guidelines and subscribe/unsubscribe info:
<a moz-do-not-send="true"
href="http://lists.ensembl.org/mailman/listinfo/dev"
target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><br>
Ensembl Blog: <a moz-do-not-send="true"
href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a><br>
<br>
</blockquote>
</div>
<br>
</div>
</div>
</div>
<br>
_______________________________________________<br>
Dev mailing list <a moz-do-not-send="true"
href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><br>
Posting guidelines and subscribe/unsubscribe info: <a
moz-do-not-send="true"
href="http://lists.ensembl.org/mailman/listinfo/dev"
target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><br>
Ensembl Blog: <a moz-do-not-send="true"
href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a><br>
<br>
</blockquote>
</div>
<br>
</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
<pre wrap="">_______________________________________________
Dev mailing list <a class="moz-txt-link-abbreviated" href="mailto:Dev@ensembl.org">Dev@ensembl.org</a>
Posting guidelines and subscribe/unsubscribe info: <a class="moz-txt-link-freetext" href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a>
Ensembl Blog: <a class="moz-txt-link-freetext" href="http://www.ensembl.info/">http://www.ensembl.info/</a>
</pre>
</blockquote>
<div class="moz-signature">
<table align="center" border="0" cellpadding="0">
<tbody>
<tr>
<td><br>
</td>
<td><br>
</td>
</tr>
</tbody>
</table>
<div align="center">
<hr align="center" size="2" width="100%"> </div>
</div>
</body>
</html>